Just before his torturers pushed him out of the van, barely conscious, on to the Nairobi pavement, Abdi was told he was one of the lucky ones: “You were supposed to die tonight.”

The security operatives who picked him up were Kenyan, but new research from the Angaza Foundation for African Reporting suggests they are part of a US-funded counter-terrorism strategy across Africa that is leaving a trail of destruction in its wake.

The security forces, in particular the Kenyan Defence Force, which continues to receive significant US funding, and the anti-terrorism police unit, have been accused of torture and summary executions.

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Though the nature of Abdi’s account makes it difficult to independently verify, the details are similar to those of other accounts collected by local NGOs, including the Independent Medico-Legal Unit, which documents incidents of torture and political violence in Kenya.

Abdi said he was walking out of the university where he studied in 2015 when a car, modified to operate as a mobile torture unit, pulled up next to him, and a gun with a silencer was pointed at his face.

As Abdi was restrained he was told by men who identified themselves as police that he had been under surveillance for years. His interrogators were suspicious because he was living in a house outside Eastleigh, Nairobi’s predominantly Somali suburb. They kept asking: “Are you trying to recruit for al-Shabaab?”

Whenever they did not like an answer they shocked him with an industrial cattle prod, he says, estimating that the whole ordeal lasted for seven hours.

Abdi now suffers chronic back pain from the shocks. But still, he considers himself one of the lucky ones. “Out of 10 [people] taken, maybe one comes back,” he says.

Dr Abdallah Waititu was less fortunate. He left work on the afternoon of 4 April last year and has not been seen since. The 33-year-old pharmacist of Somali origin, known as Duktur (doctor), was a pillar of the Eastleigh community until he vanished.

“Our friends tell us not to worry, that he’s still alive. But I can’t believe it until I see him,” said his brother Imran. For Waititu’s grieving family, life has changed drastically. His three wives and five young children have had to move into a smaller apartment, and his brothers work overtime to cover rent and food. Every week, they do the rounds of local police stations and morgues.

The family are also trying to sue the government to get it to reveal where Waitutu is. The government says it does not know.

In June, Abdul Mwangi Karuri, another senior figure at the mosque and a budding politician, also disappeared. His colleagues at the Democratic party blame the authorities. Kenyan officials, including the National Counter-terrorism Centre, did not respond to repeated requests to comment on either case.

Stories of intimidation, arrests, torture and disappearances have become the norm in Eastleigh, but Imran believes “Kenya is just doing this to please the outside world. Every abduction is proof to donors that their money is being spent”, he said.

Examples of the tension between fighting terror and protecting human rights span the continent: in Nigeria, the US is spending $40m to fight Boko Haram, despite the State Department’s own findings that Nigeria’s “security services perpetrated extrajudicial killings, and engaged in torture [and] rape”.

In South Sudan, US funding before the outbreak of civil war in 2013 helped to train and modernise the national army, despite the widespread use of child soldiers.

There is also the Trans-Saharan Counter-terrorism Partnership, a flagship initiative that since 2005 has given between $90m and $160m from the US government a year to security forces and judicial services across 10 countries in the Sahel and Maghreb: Algeria, Burkina Faso, Chad, Mauritania, Mali, Morocco, Niger, Nigeria, Senegal, and Tunisia – many with dubious respect for democracy and freedom.

Kenya is a particularly striking example of this schism. In 2016 the US gave $120m worth of support to the Kenyan military and $8m to the police. The same year, Human Rights Watch documented 34 enforced disappearances in Nairobi and north-east Kenya linked to counter-terrorism operations.

Constitutionally, the US is not supposed to fund human rights abusers. According to the Leahy law, pushed through by the senator Patrick Leahy in the late 1990s, “no assistance shall be furnished … to any unit of the security forces of a foreign country if the secretary of state has credible information that such unit has committed a gross violation of human rights”.

The wording is the downfall. By specifying assistance by unit it presumes that the good cops can be separated, and funded separately, from bad cops. Human Rights Watch says this loophole is being exploited in countries such as Kenya. Requests for specific information about how the US funds Kenya’s security services were made to the Department of State, Department of Defence, and the US embassy in Kenya, but were all rebuffed or ignored.

The US Africa Command, responsible for military relations on the continent, said that “funding assistance is generally denied in those cases where there is determined to be credible information that such members or units of a foreign security force have committed a gross violation of human rights”.

The majority of members, from al-Shabaab and the Mombasa Republican Council (MRC), “referred to injustices at the hands of Kenyan security forces”, explains Anneli Botha, the researcher on the project.

Some complained that “all Muslims are treated as terrorists”, while others pointed to specific failings by the Kenyan police.

A year after his interrogation Abdi says he no longer walks around in fear, but feels angry and betrayed. “The people I’m supposed to run to for protection, they are the ones attacking me. They are supposed to fight terror, but they are the terrorists,” he says.

This story was supported by the Angaza Foundation for African Reporting